The kernel update might be possibility.

I am now running 4.9.0 custom built, and the system / screen is not freezing,
but instead sometimes Xorg crashes, usually when clicking something. I am able
to reproduce it reliably on some webpages in chrome, when clicking specifying
button (dmesg shows X11 segfault, but entire Xorg exits, and I need to
relogin). I was able to also reproduce it in few other programs like VLC, but
less reliably.

Probably a different issue.

It is also possibly that my Xorg server is now confused, and uses i915 instead
of radeon (ThinkPad W500 has both), but dmesg and xorg.0.log claims I am using
radeon, but glxinfo shows there is no hardware opengl acceleration (llvmpipe
instead). Weird.

I will try to reproduce it again, maybe on 4.8 kernel again.